Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-12
Subjects
- Location of subjects
- Australia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- crohn disease ASCA negative patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- crohn disease ASCA positive patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Crohn disease anti-Saccharomyces cerevisiae antibody status
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Non-quantitative PCR
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-12
Source: Figure 1
Description: Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients
Abundance in Group 1: increased abundance in crohn disease ASCA positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| [Ruminococcus] torques |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-12
Source: Figure 1
Description: Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients
Abundance in Group 1: decreased abundance in crohn disease ASCA positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter cloacae | ||
| Faecalibacterium prausnitzii |
Revision editor(s): WikiWorks
